Planning Your Installation

Installation of lorax under linux can be done either via a direct install (using either build scripts we supply or using your distribution’s package manager) or an indirect install via Anaconda Python and packages in the bioconda channel. Which path you choose depends on your OS and general preferences. If you are installing on BSD, direct installs are your only choice as Anaconda Python is not available for this platform. If you are installing on a Mac, you will need a number of prerequisites that are most easily satisfied via Anaconda Python packages. If you are installing on linux, Anaconda Python will get you up and running more quickly while direct installs are more heavily tested and will give you more control of the installation. This is especially important if you anticipate using RAxML heavily and you wish to take advantage of AVX/AVX2 hardware.

MacOS Installation

lorax was tested under MacOS Sierra (10.12.6). The minimum OS version for proper function of Anaconda Python is MacOS 10.12.3.

Installation of lorax under MacOS requires use of git. To test if you have git installed, open a terminal window (under Applications -> Utilities) and issue the command:

git --version

If this produces an error, the easiest way to install git is by installing the XCode command-line tools, part of the XCode utilities, which are available for free (but large) download from the App Store.

Besides the XCode tools, you will also need to install gcc (because the current Mac clang does not include OpenMP) as well as the PCRE and OpenSSL libraries. The tested configuration was with PCRE-8.40 and OpenSSL-1.10.f. Both libraries were configured with CC=clang and installed to /usr/local.